How to Identify Hidden Calcium Deficiency: A Functional Medicine Approach

Calcium isn’t just for strong bones. It’s essential for nerve function, muscle contraction, hormone balance, enzyme activity, and blood clotting.

Most people think calcium deficiency only shows up in severe diseases like osteoporosis or rickets—but subtle, suboptimal calcium levels can quietly affect health long before that, contributing to issues like:

Osteopenia and osteoporosis
High blood pressure
Sleep problems
Autoimmune conditions
Low sex hormones

The problem? Standard serum calcium tests often miss these early deficiencies. That’s why functional medicine takes a more nuanced approach.

Why Serum Calcium Isn’t Enough

Your body tightly controls calcium in the blood, keeping levels steady even when dietary intake is low.

Only 1% of your body’s calcium is in the blood and tissues.
The other 99% is stored in bones and teeth, making serum calcium a poor marker for subtle deficiencies.

Low serum calcium usually appears only in severe deficiencies or in conditions like advanced vitamin D deficiency or chronic kidney disease.

The Calcium-Vitamin D-PTH Connection

Calcium doesn’t act alone. It works closely with:

Vitamin D – helps absorb calcium from the gut
Parathyroid hormone (PTH) – regulates calcium release from bones
Phosphorus – competes with calcium for absorption

High phosphorus levels—often due to processed foods and additives—can block calcium absorption.
When calcium drops, PTH rises to pull calcium from bones and maintain blood levels.

A useful tip from nutrition expert Dr. Chris Masterjohn:

High calcitriol (active vitamin D) + normal serum calcium + elevated PTH often indicates a hidden calcium deficiency, even if standard labs look “normal.”

How to Detect Suboptimal Calcium

Since labs don’t always show the full picture, diet tracking is one of the best ways to assess calcium intake.

Our process:

Patients log their food and drinks for five days using the Cronometer app.
We review their calcium intake, aiming for 1,000 mg daily (or 1,200 mg for women over 50).
If intake is low, we first increase dietary calcium sources like leafy greens, sardines, almonds, and sesame seeds.
If diet alone isn’t enough—or absorption issues like SIBO, Crohn’s, or celiac disease are present—we consider a whole bone calcium supplement, which mimics dietary sources and is well absorbed.

Populations at Higher Risk

Certain groups are more prone to calcium deficiency and should be monitored closely:

Vegetarians and vegans
Postmenopausal women
People with lactose intolerance or milk allergies
Those with chronic digestive disorders or malabsorption issues

Key Takeaways

Calcium plays a critical role beyond bone health, affecting hormones, nerves, and immunity.
Serum calcium alone isn’t reliable for detecting hidden deficiencies.
Track dietary intake to assess levels, aiming for 1,000 mg/day through whole foods first.
Consider supplementation if diet and absorption are limited.
Watch for at-risk populations and address early to prevent long-term disease.

By shifting our focus to prevention and optimization, we can catch calcium issues before they lead to fractures or chronic conditions.